If it's Windows, it doesn't actually use flags for those emojis, it renders a country code instead. If it wasn't supported you would just see the glyph for an unknown character.
The reason was because they didn't want to be caught up in any arguments about what flag to render for a country during any dispute, as with, e.g. the flag for Afghanistan after the Taliban took control.
Do you have a citation for that? I suspected it was because of the political issues, so I tried hunting down the reason one day and came up blank.
[Microsoft had this same issue with the timezone map in Windows. The early versions were cool and had country borders, but then I think it was India/Pakistan threw a fit and it was simplified to take the borders out]
The reason was because they didn't want to be caught up in any arguments about what flag to render for a country during any dispute, as with, e.g. the flag for Afghanistan after the Taliban took control.